Pleistocene climatic fluctuations drive isolation and secondary contact in the red diamond rattlesnake (Crotalus ruber) in Baja California

Abstract

Aim: Many studies have investigated the phylogeographic history of species on the Baja California Peninsula, and they often show one or more genetic breaks that are spatially concordant among many taxa. These phylogeographic breaks are commonly attributed to vicariance as a result of geological or climatic changes, followed by secondary contact when barriers are no longer present. We use restriction-site associated DNA sequence data and a phylogeographic model selection approach to explicitly test the secondary contact hypothesis in the red diamond rattlesnake, Crotalus ruber.Location: Baja California and Southern California. Methods:We used phylogenetic and population clustering approaches to identify population structure. We then used coalescent methods to simultaneously estimate population parameters and test the fit of phylogeographic models to the data. We used ecological niche models to infer suitable habitat for C. ruber at the Last Glacial Maximum (LGM).Results: Crotalus ruber is composed of distinct northern and southern populations with a boundary near the town of Loreto in Baja California Sur. A model of isolation followed by secondary contact provides the best fit to the data, with both divergence and contact occurring in the Pleistocene. We also identify a genomic signature of northern range expansion in the northern population, consistent with LGM niche models showing that the northern-most portion of the range of C. ruber was not suitable habitat during the LGM. Main conclusions:We provide the first explicitly model-based test of the secondary contact model in Baja California and show that populations of C. ruber were isolated before coming back into contact near Loreto, a region that shows phylogeographic breaks for other taxa. Given the timing of divergence and contact, we suggest that climatic fluctuations have driven the observed phylogeographic structure observed in C. ruber and that they may have driven similar patterns in other taxa. Grismer, 2002;Lindell, M endez-De La Cruz, & Murphy, 2008;Riddle, Hafner, Alexander, & Jaeger, 2000;Savage, 1960;Zink, 2002) (Aguirre, Morafka, & Murphy, 1999;Murphy, 1983).However, this hypothesis has been weakened by a general lack of direct geological evidence and the finding that mid-peninsular divergences indicate at least two episodes of divergence (Crews & Hedin, 2006;Dolby et al., 2015;Leach e, Crews, & Hickerson, 2007). No strong evidence has been presented to suggest that a seaway crossed the peninsula in the vicinity of Loreto, leaving the drivers of spatially concordant phylogenetic and phylogeographic breaks unclear at all of these regions.The phylogeographic patterns observed could be produced by at least two different processes: (1) Here, we sought to examine the phylogeography of mainland populations of Crotalus ruber (the red diamond rattlesnake), a large rattlesnake that ranges throughout Baja California and into southern California (Figure 1), using genomic data and explicit testing of alternative phylogeographic models. We also inv...

Biogeographic barriers, Pleistocene refugia, and climatic gradients in the southeastern Nearctic drive diversification in cornsnakes (Pantherophis guttatus complex)

“…In these models, we fixed the topology of the four populations based on the results from SNAPP and we fixed the initial divergence time within this group and the divergence between P. emoryi and P. slowinskii at 2.97 mya and 590 kya, respectively (Chen, Lemmon, Lemmon, Pyron, & Burbrink, ). These models also allowed for recent gene flow between adjacent populations and we used a mutation rate of 7.26 × 10 –9 (Harrington, Hollingsworth, Higham, & Reeder, ) assuming a 3‐year generation time (estimate for P. emoryi ; Ernst & Ernst, ). The two‐population models differ only in the parameterization of gene flow between the ancestral lineages (see Figure a), such that these models are simplifications of isolation with migration (Figure a—IM) or, alternatively, in strict allopatry across the Mississippi River (Figure a—ISO).…”

Comparative phylogenomic patterns in the Baja California avifauna, their conservation implications, and the stages in lineage divergence

“…However, the phylogeographic breaks are not all consistent. For example, Harrington et al (2018) found a different genetic division in a rattlesnake, Crotalus ruber, centered south of the Vizcaino Desert and they concluded there was secondary contact with northward gene flow. These patterns also contrast with other species, such as the California gnatcatcher (Polioptila californica), which prior data have shown shows no apparent divisions across Baja (Zink et al 2000(Zink et al , 2013.…”

“…In theory, species existing over the same area ought to have experienced the same geological history and display concordant phylogeographic patterns (Bermingham and Mortiz, 1998). However, if some species are recent arrivals to the region, differ in their ability to disperse across biogeographic barriers, or possess different effective population sizes then phylogeographic patterns may differ (Zink, 2002(Zink, , 2010Harrington et al, 2018). As a result, codistributed species can exhibit shallow, strong, or no divergence across a common geographic area.…”

Latitudinal divergence in a widespread amphibian: Contrasting patterns of neutral and adaptive genomic variation

“…The central‐margin hypothesis puts forward qualitatively similar predictions where the highest genetic variation is expected to be harboured at the core of the species range, decreasing from the core towards the range margin (Brown, ; Eckert et al, ; Guo, ). Furthermore, at secondary contact zones between previously isolated lineages there is room for both neutral and adaptive gene flow (Carvalho et al, ; Harrington, Hollingsworth, Higham, & Reeder, ; Linnen, Kingsley, Jensen, & Hoekstra, ), which may lead to a nonlinear relationship between genetic variation and latitude.…”